[Biopython-dev] [Bug 1762] Bio.GenBank.FeatureParser dislikes valid accessions and locus lines

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Mon Nov 21 10:13:27 EST 2005


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
 Attachment #247 is|0                           |1
           obsolete|                            |
         AssignedTo|biopython-dev at biopython.org |biopython-
                   |                            |bugzilla at maubp.freeserve.co.
                   |                            |uk
             Status|NEW                         |ASSIGNED

------- Comment #8 from biopython-bugzilla at maubp.freeserve.co.uk  2005-11-21 10:13 -------
Created an attachment (id=252)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=252&action=view)
Bio/GenBank/__init__.py patch

Patches to my non-martel GenBank parser to:

(1) tackle the truncated LOCUS line problem (i.e. this bug)
(2) tackle missing features as in seqret output (i.e. this bug)

Plus a few changes that should be on bug 1899 really:

(3) started to split the feed function into sub functions
(4) minor changes to comments to remove references to Martel
(5) removed the ErrorParser class used by the Martel parser

And fix for bug 1903 as well:

(6) GenBank parses fails with unusual quoting and line breaks

The genbank unit test still works.

Michiel - could you create another (smaller) seqret file to go in the GenBank
unit tests?

------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.
You are the assignee for the bug, or are watching the assignee.

More information about the Biopython-dev mailing list